HEADER HYDROLASE 20-MAY-17 5O2E TITLE CRYSTAL STRUCTURE OF NDM-1 IN COMPLEX WITH HYDROLYZED CEFUROXIME - NEW TITLE 2 REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE TYPE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: B2 METALLO-BETA-LACTAMASE,BETA-LACTAMASE TYPE II,METALLO- COMPND 5 BETA-LACTAMASE NDM-1,METALLO-BETA-LACTAMASE TYPE II,NEW DELHI COMPND 6 METALLO-BETA-LACTAMASE-1,NDM-1; COMPND 7 EC: 3.5.2.6; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, NDM-1, METALLO-BETA-LACTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.RACZYNSKA,I.G.SHABALIN,M.JASKOLSKI,W.MINOR,A.WLODAWER REVDAT 4 22-FEB-23 5O2E 1 SPRSDE REVDAT 3 02-NOV-22 5O2E 1 REMARK LINK REVDAT 2 16-OCT-19 5O2E 1 SPRSDE REMARK REVDAT 1 26-DEC-18 5O2E 0 JRNL AUTH J.E.RACZYNSKA,I.G.SHABALIN,W.MINOR,A.WLODAWER,M.JASKOLSKI JRNL TITL A CLOSE LOOK ONTO STRUCTURAL MODELS AND PRIMARY LIGANDS OF JRNL TITL 2 METALLO-BETA-LACTAMASES. JRNL REF DRUG RESIST. UPDAT. V. 40 1 2018 JRNL REFN ESSN 1532-2084 JRNL PMID 30466711 JRNL DOI 10.1016/J.DRUP.2018.08.001 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.FENG,J.DING,D.ZHU,X.LIU,X.XU,Y.ZHANG,S.ZANG,D.C.WANG,W.LIU REMARK 1 TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO NDM-1 CATALYZED REMARK 1 TITL 2 HYDROLYSIS OF CEPHALOSPORINS. REMARK 1 REF J. AM. CHEM. SOC. V. 136 14694 2014 REMARK 1 REFN ESSN 1520-5126 REMARK 1 PMID 25268575 REMARK 1 DOI 10.1021/JA508388E REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 88894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : COPIED FROM 4RL0 REMARK 3 R VALUE (WORKING + TEST SET) : 0.103 REMARK 3 R VALUE (WORKING SET) : 0.101 REMARK 3 FREE R VALUE : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4618 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5994 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.1290 REMARK 3 BIN FREE R VALUE SET COUNT : 298 REMARK 3 BIN FREE R VALUE : 0.1740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3549 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 676 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.041 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.125 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3883 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3641 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5317 ; 1.625 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8374 ; 0.990 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 512 ; 6.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;31.980 ;24.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 597 ;11.643 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.274 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 596 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4614 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 885 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1963 ; 1.874 ; 1.095 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1964 ; 1.875 ; 1.095 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2459 ; 2.193 ; 1.642 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2460 ; 2.193 ; 1.643 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1920 ; 3.058 ; 1.415 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1921 ; 3.059 ; 1.416 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2843 ; 3.376 ; 1.999 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4985 ; 4.265 ;11.860 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4986 ; 4.264 ;11.861 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7513 ; 1.658 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 123 ;29.013 ; 0.100 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7951 ; 9.444 ; 0.100 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5O2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG3350, 0.1M BIS-TRIS PH REMARK 280 6.0 AND 0.2 M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.59000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.53000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.53000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.59000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.44500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -201.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 ILE A 31 REMARK 465 GLY A 36 REMARK 465 GLN A 37 REMARK 465 GLY B 29 REMARK 465 GLU B 30 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 38 CG CD OE1 NE2 REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 600 O HOH A 610 2.06 REMARK 500 O HOH A 501 O HOH A 578 2.07 REMARK 500 O HOH A 413 O HOH A 588 2.16 REMARK 500 O HOH A 712 O HOH A 731 2.16 REMARK 500 O HOH B 550 O HOH B 732 2.18 REMARK 500 OD2 ASP B 223 O HOH B 401 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLY A 83 O HOH B 637 2555 1.94 REMARK 500 O HOH A 408 O HOH B 636 3545 2.09 REMARK 500 O HOH A 676 O HOH B 738 3655 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 264 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 90 141.87 73.89 REMARK 500 ASP B 90 145.42 73.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 724 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 725 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 726 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 727 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 728 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 729 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 730 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 731 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 732 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A 733 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH B 743 DISTANCE = 5.97 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 97.9 REMARK 620 3 HIS A 189 NE2 100.8 116.0 REMARK 620 4 HOH A 438 O 102.0 120.7 114.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 102.7 REMARK 620 3 HIS A 250 NE2 86.7 102.5 REMARK 620 4 3S0 A 304 NAR 93.8 160.1 89.4 REMARK 620 5 3S0 A 304 OAX 163.1 93.9 86.9 70.6 REMARK 620 6 HOH A 438 O 81.8 92.8 162.5 78.3 100.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 98.4 REMARK 620 3 HIS B 189 NE2 103.2 116.2 REMARK 620 4 HOH B 459 O 104.9 119.4 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 102.3 REMARK 620 3 HIS B 250 NE2 87.1 102.6 REMARK 620 4 3S0 B 304 NAR 94.2 160.8 87.6 REMARK 620 5 3S0 B 304 OAY 163.6 93.8 86.6 70.4 REMARK 620 6 HOH B 459 O 82.1 94.2 161.6 78.4 99.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues 3S0 A 304 and UNL A REMARK 800 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues UNL B 301 and 3S0 B REMARK 800 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RL0 RELATED DB: PDB REMARK 900 RE-REFINEMENT OF ENTRY 4RL0 DBREF 5O2E A 29 270 UNP C7C422 BLAN1_KLEPN 29 270 DBREF 5O2E B 29 270 UNP C7C422 BLAN1_KLEPN 29 270 SEQRES 1 A 242 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 A 242 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 A 242 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 A 242 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 A 242 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 A 242 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 A 242 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 A 242 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 A 242 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 A 242 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 A 242 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 A 242 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 A 242 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 A 242 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 A 242 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 A 242 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 A 242 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 A 242 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 A 242 ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 242 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR SEQRES 2 B 242 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU SEQRES 3 B 242 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET SEQRES 4 B 242 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL SEQRES 5 B 242 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP SEQRES 6 B 242 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS SEQRES 7 B 242 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR SEQRES 8 B 242 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU SEQRES 9 B 242 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER SEQRES 10 B 242 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN SEQRES 11 B 242 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO SEQRES 12 B 242 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR SEQRES 13 B 242 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY SEQRES 14 B 242 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE SEQRES 15 B 242 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP SEQRES 16 B 242 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE SEQRES 17 B 242 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER SEQRES 18 B 242 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR SEQRES 19 B 242 ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET SO4 A 303 5 HET 3S0 A 304 26 HET UNL A 305 1 HET UNL B 301 1 HET ZN B 302 1 HET ZN B 303 1 HET 3S0 B 304 26 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM 3S0 (2R,5S)-5-[(CARBAMOYLOXY)METHYL]-2-[(R)-CARBOXY{[(2Z)- HETNAM 2 3S0 2-(FURAN-2-YL)-2-(METHOXYIMINO)ACETYL]AMINO}METHYL]-5, HETNAM 3 3S0 6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID HETNAM UNL UNKNOWN LIGAND FORMUL 3 ZN 4(ZN 2+) FORMUL 5 SO4 O4 S 2- FORMUL 6 3S0 2(C16 H18 N4 O9 S) FORMUL 12 HOH *676(H2 O) HELIX 1 AA1 THR A 94 ILE A 109 1 16 HELIX 2 AA2 HIS A 122 GLY A 127 1 6 HELIX 3 AA3 GLY A 128 ALA A 135 1 8 HELIX 4 AA4 ALA A 143 ALA A 149 1 7 HELIX 5 AA5 PRO A 150 GLY A 153 5 4 HELIX 6 AA6 GLU A 170 ALA A 174 5 5 HELIX 7 AA7 HIS A 228 PHE A 240 1 13 HELIX 8 AA8 ARG A 256 LYS A 268 1 13 HELIX 9 AA9 THR B 94 ILE B 109 1 16 HELIX 10 AB1 HIS B 122 GLY B 127 1 6 HELIX 11 AB2 GLY B 128 ALA B 135 1 8 HELIX 12 AB3 ALA B 143 ALA B 149 1 7 HELIX 13 AB4 PRO B 150 GLY B 153 5 4 HELIX 14 AB5 GLU B 170 ALA B 174 5 5 HELIX 15 AB6 CYS B 208 ILE B 210 5 3 HELIX 16 AB7 HIS B 228 PHE B 240 1 13 HELIX 17 AB8 ARG B 256 LYS B 268 1 13 SHEET 1 AA1 8 ASP A 43 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 AA1 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 AA1 8 GLY A 71 ASP A 82 -1 O GLY A 71 N MET A 67 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 AA1 8 VAL A 113 VAL A 117 1 O VAL A 117 N VAL A 88 SHEET 7 AA1 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA1 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA2 4 LEU A 180 PHE A 183 0 SHEET 2 AA2 4 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181 SHEET 3 AA2 4 ILE A 203 GLY A 207 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 MET A 248 1 O VAL A 247 N GLY A 206 SHEET 1 AA3 8 GLN B 44 PHE B 46 0 SHEET 2 AA3 8 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 3 AA3 8 VAL B 58 MET B 67 -1 O GLN B 60 N ARG B 52 SHEET 4 AA3 8 GLY B 71 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 5 AA3 8 ARG B 85 VAL B 89 -1 O ARG B 85 N ASP B 82 SHEET 6 AA3 8 VAL B 113 VAL B 117 1 O ALA B 114 N VAL B 86 SHEET 7 AA3 8 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 8 AA3 8 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 AA4 4 LEU B 180 PHE B 183 0 SHEET 2 AA4 4 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181 SHEET 3 AA4 4 ILE B 203 GLY B 207 -1 O PHE B 205 N VAL B 196 SHEET 4 AA4 4 MET B 245 MET B 248 1 O VAL B 247 N GLY B 206 LINK CAZ 3S0 A 304 CL UNL A 305 1555 1555 1.84 LINK CL UNL B 301 CAZ 3S0 B 304 1555 1555 1.87 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.09 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.00 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.03 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.02 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.35 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.14 LINK ZN ZN A 301 O HOH A 438 1555 1555 1.98 LINK ZN ZN A 302 NAR 3S0 A 304 1555 1555 2.37 LINK ZN ZN A 302 OAX 3S0 A 304 1555 1555 2.12 LINK ZN ZN A 302 O HOH A 438 1555 1555 2.12 LINK NE2 HIS B 120 ZN ZN B 302 1555 1555 2.07 LINK ND1 HIS B 122 ZN ZN B 302 1555 1555 2.00 LINK OD2 ASP B 124 ZN ZN B 303 1555 1555 2.01 LINK NE2 HIS B 189 ZN ZN B 302 1555 1555 1.98 LINK SG CYS B 208 ZN ZN B 303 1555 1555 2.34 LINK NE2 HIS B 250 ZN ZN B 303 1555 1555 2.12 LINK ZN ZN B 302 O HOH B 459 1555 1555 1.99 LINK ZN ZN B 303 NAR 3S0 B 304 1555 1555 2.35 LINK ZN ZN B 303 OAY 3S0 B 304 1555 1555 2.15 LINK ZN ZN B 303 O HOH B 459 1555 1555 2.12 SITE 1 AC1 5 HIS A 120 HIS A 122 HIS A 189 3S0 A 304 SITE 2 AC1 5 HOH A 438 SITE 1 AC2 5 ASP A 124 CYS A 208 HIS A 250 3S0 A 304 SITE 2 AC2 5 HOH A 438 SITE 1 AC3 2 ARG A 270 HOH A 593 SITE 1 AC4 5 HIS B 120 HIS B 122 HIS B 189 3S0 B 304 SITE 2 AC4 5 HOH B 459 SITE 1 AC5 5 ASP B 124 CYS B 208 HIS B 250 3S0 B 304 SITE 2 AC5 5 HOH B 459 SITE 1 AC6 21 LEU A 65 MET A 67 TRP A 93 HIS A 122 SITE 2 AC6 21 GLN A 123 ASP A 124 GLU A 152 HIS A 189 SITE 3 AC6 21 CYS A 208 LYS A 211 GLY A 219 ASN A 220 SITE 4 AC6 21 HIS A 250 ZN A 301 ZN A 302 HOH A 438 SITE 5 AC6 21 HOH A 586 PRO B 68 GLY B 69 PHE B 70 SITE 6 AC6 21 HOH B 601 SITE 1 AC7 16 GLY A 69 PHE A 70 LEU B 65 HIS B 122 SITE 2 AC7 16 GLN B 123 ASP B 124 HIS B 189 CYS B 208 SITE 3 AC7 16 LYS B 211 GLY B 219 ASN B 220 HIS B 250 SITE 4 AC7 16 ZN B 302 ZN B 303 HOH B 459 HOH B 599 CRYST1 39.180 78.890 133.060 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007515 0.00000